Those items are still vegan. That warning is put there mostly for people who have allergies to those items so that they can be aware of this. If one were to avoid eating food that was processed in a facility (or agricultural field where natural manure etc is used) it would be very very difficult to remain "pure" vegan. Similarly, there are very few all vegan groceries, but buying food in a mainstream store or whole foods store doesn't mean you aren't vegan either.